1. Field of the Invention
The present invention relates generally to the fields of microarray technology and population genotyping. More specifically, the present invention relates to a portable system and method of real-time high throughput population-scale HLA genotyping in a field environment.
2. Description of the Related Art
Bioterrorism and military interests have compelled the Department of Homeland Defense to invest heavily in high speed, flexible and high capacity methods of vaccine development. Recent studies have begun to confirm what basic immunology had predicted, namely that, within a large exposed population, individual response to infection and individual response to vaccination may vary greatly as a function of HLA type (1-2). However, only a few such studies have been performed to date, in part because HLA typing has been too expensive to implement as part of the epidemiology of infectious disease or the clinical epidemiology of vaccine development. Moreover, from the viewpoint of Homeland Defense, even if a thorough knowledge of the relationship between HLA type and infection or vaccine response were known, and even if “personalized” vaccines were available based on the HLA type, the current technologies for HLA-typing do not have rapid field response capability and are too expensive and too complicated to be implemented in the context of a population-scale emergency.
Human immunogenic response to pathogens and vaccinations is dependent on the HLA loci. The response to pathogens is due to two distinct classes of polymorphic cell surface glycoproteins that are encoded by the HLA loci (3). HLA class I molecules identify the endogenous antigen present in the cytoplasm due to infection by bacteria or viruses and present it to the CD8+ cytotoxic T lymphocytes which kill the infected cells. HLA class II molecules also tag the infected cells by displaying exogenously derived epitopes on the surface of antigen-presenting cells for CD4+ helper T cells which results in an immune response against an invading pathogen. A diverse range of specificities for the epitope-HLA-Binding interaction is dependent on the extensive polymorphisms at the HLA loci.
Polymorphisms at the HLA loci are brought about by recombination, gene conversion and mutation and their natural selection in response to pathogens and infectious diseases (4). Hence, a diversity of HLA alleles enhances human ability to respond to and resist infectious and pathogenic agents at the population scale. HLA polymorphisms have been associated with several diseases and most recently with resistance to AIDS virus (5). Since most of the viral vaccines are viral surface antigens in a low dose, one's ability to react to such a vaccination is dependent on the polymorphism at the HLA loci. For example, the haplotype HLA-B8, SC01, DR3 lacks a response gene for hepatitis B virus surface antigen (6). In order to develop a vaccination it is very vital to find out the HLA type and classify the vaccine response to a set of known haplotypes.
The traditional serological methods for HLA typing have been limited to the availability of the allele-specific sera to identify structural differences due to single nucleotide polymorphisms (7). The antibodies used in the conventional methods are specific to HLA surfaces. However, structural differences in the peptide binding groove of HLA heavy chain due to single or multiple nucleotide polymorphisms cannot be easily identified using the antibody-based methods.
Nucleic acid based methods utilize sequence specific oligonucleotide probes (SSOP) or sequence specific primers (SSP). The sequence specific oligonucleotide probe method is based on the use of either individual DNA samples or sequence specific oligonucleotide probes to identify the polymorphism (8). Current methods of primer design rely on simple BLAST like alignments to identify the primers and do not always perform well to pick out the unique primer set. Individual primers identified as specific to the loci are used to amplify the whole locus and specific probes are used to identify the polymorphism.
These are tiered approaches where the resolution is low to medium, and high resolution can be achieved by further probing with specific probes. The two versions of this method are dot blot where the DNA sample is immobilized on a membrane support and a labeled sequence specific oligonucleotide probe is allowed to hybridize to identify the polymorphism in the immobilized sample or a reverse dot blot where the sequence specific oligonucleotide probe is immobilized and a labeled DNA sample is added to the sequence specific oligonucleotide probe to identify the polymorphism. Immobilization of sequence specific oligonucleotide probes allows the testing of several polymorphisms, where as the immobilization of the DNA sample allows the testing of several samples for a specific polymorphism.
The sequence specific primer method uses specific primers targeted to each of the polymorphism (9). The number of primers required for the analysis of a locus depends on the number of polymorphisms in that particular locus. Typically, a large number of PCR reactions are needed to complete the HLA typing. This is a PCR based method where the presence or absence of a polymorphism results in amplification of the product. Using conventional gel electrophoresis the presence or absence of the PCR product can be ascertained. The PCR reactions contain positive control primers that amplify conserved regions.
Other methods are structure based or utilize sequencing methods. A structure-based method to identify polymorphisms is based on the fact that mismatched heteroduplexes containing looped out regions migrated differently than a heteroduplex without any mismatched loops in a non-denaturing gel (10). With the automation of DNA sequencing, HLA typing has been done on sequencing machines (11-12). The methodology is dependent on the number of polymorphisms and the number of exons, for example, for HLA class II the polymorphisms are in exon 2 which has a few hundred bases. In contrast, for class I typing the polymorphisms require several exons to be sequenced and hence become more complicated and can result in errors.
Single nucleotide polymorphisms in the HLA types are shared by the several subtypes of the alleles. This could result in ambiguities when the conventional methods are used. In order to overcome this problem due to cross hybridization, a combination of probes and primers combined with the knowledge of the polymorphisms is essential. Hence, a simple SSOP or sequence specific primer hybridization might not result in the assignment of the HLA type.
The accurate assignment of HLA types is then based on carefully sifting through the patterns of a combination of probes for several subtypes. A PCR based method or a dot blot method would require a high amount of sample and would turn out to be very costly. Thus, a miniaturized technique that requires less amount of sample and is economical is needed. Microarrays (13) in combination with pattern recognition software provide such a platform to generate a 2-dimensional barcode to unambiguously identify the HLA type.
Microarrays are suited ideally for the high-throughput requirements in HLA typing. They offer the convenience of miniaturization and the ability to perform thousands of hybridizations in a single experiment. This highly parallel nature of the microarrays and their unique format makes them ideally suited for field use. In spite of these potential benefits, microarrays have not been perfected for field use in HLA typing. Cost, quality, and portability are among the limiting factors and are dependent on the method of manufacture.
Current microarrays in the market use specific dyes and so a specific type of imager needs to be used. Ideally, an imager should be able to image any dye. Also, current imagers in the market are not portable. Additionally, current analysis packages are equally cumbersome to use and require some manual intervention to identify the patterns.
The first olignucleotide microarray for the detection of allelic variants was reported in 1989 (14). Sequence specific oligonucleotide probes were spotted onto nylon membranes and hybridized to biotinylated CR products of the DNA samples. Genotype of the alleles was identified using the color intensity of the spots. More recently another study reported the use of a 130 probe element DNA microarrays to identify the allelic variations of class II polymorphisms (15). While the applicability of the microarrays to obtain medium to high resolution HLA typing is obvious, the technology in its current form still suffers from several limitations, both technical and economical.
Additionally, using conventional methods, e.g., sequence specific oligonucleotide probes, the DNA sample is double stranded and the probe is single stranded. The presence of a double stranded product reduces the efficiency of hybridization. T7 or T3 polymerase sequences have been used to create single-stranded target molecules by in vitro transcription. Labeling RNA is difficult and hence the amplification methods utilize an end-labeled primer with biotin or a fluorescent dye so that all of the product can be labeled. The presence of biotin could interfere with the amplification procedure.
Furthermore, a significant limitation to performing population-scale HLA typing is the collection of the samples. Traditional methods of sample collection have focused on a blood draw of 10-15 ml by invasive procedures. This form of collection leads to a degradation, contamination and inaccurate results. Blood samples collected in this way would require a large scale handling, storage, and transportation problems that enormously increase the cost and logistical complexity of HLA typing. In addition to the handling and collection problems with the blood draw methods, the storage of isolated DNA becomes an issue. Hence, any technology for population-scale HLA typing must have alternate methods for sample collection and archiving the extracted DNA.
There is a need in the art for improvements in systems and methods for population-scale genotyping. Specifically, the prior art is deficient in a low cost, mass-produced and field-ready portable microarray system using advanced methods of genome analysis for rapid-response HLA typing of large populations. The present invention fulfills this long-standing need and desire in the art.